RT Journal Article
SR Electronic
T1 The Genetic Landscape of Transcriptional Networks in a Combined Haploid/Diploid Plant System
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 007153
DO 10.1101/007153
A1 J.-P. Verta
A1 C.R. Landry
A1 J. MacKay
YR 2014
UL http://biorxiv.org/content/early/2014/07/15/007153.abstract
AB Heritable variation in gene expression is a source of evolutionary change and our understanding of the genetic basis of expression variation remains incomplete. Here, we dissected the genetic basis of transcriptional variation in a wild, outbreeding gymnosperm (Picea glauca) according to linked and unlinked genetic variants, their allele-specific (cis) and allele non-specific (trans) effects, and their phenotypic additivity. We used a novel plant system that is based on the analysis of segregating alleles of a single self-fertilized plant in haploid and diploid seed tissues. We measured transcript abundance and identified transcribed SNPs in 66 seeds with RNA-seq. Linked and unlinked genetic effects that influenced expression levels were abundant in the haploid megagametophyte tissue, influencing 48% and 38% of analyzed genes, respectively. Analysis of these effects in diploid embryos revealed that while distant effects were acting in trans consistent with their hypothesized diffusible nature, local effects were associated with a complex mix of cis, trans and compensatory effects. Most cis effects were additive irrespective of their effect sizes, consistent with a hypothesis that they represent rate-limiting factors in transcript accumulation. We show that trans effects fulfilled a key prediction of Wright s physiological theory, in which variants with small effects tend to be additive and those with large effects tend to be dominant/recessive. Our haploid/diploid approach allows a comprehensive genetic dissection of expression variation and can be applied to a large number of wild plant species.